Ni Neil,
There is Galaxy Reports app all that runs as a separate web app and is
generally available at galaxy instance/reports URL. It's config file
needs to be configured to point to your Galaxy instance database (see
reports_wsgi.ini in Galaxy's home dir) and the app launched
via run_reports.sh.
/cloudman/commits/all?search=a6bf542%3Acc55ca9
from
4 contributors*.
Enjoy and please let us know what you think,
Enis Afgan https://wiki.galaxyproject.org/EnisAfgan and Dannon
Bakerhttps://wiki.galaxyproject.org/DannonBaker
Galaxy Team
Hi Katie,
For genomes that are not available on Galaxy Main (or general questions you
might have about Galaxy), it's best to send an email to the galaxy-user
mailing list (CC'd now). You can subscribe to the mailing list here
http://lists.bx.psu.edu/listinfo/galaxy-user
As far as the particular
Hi Yan,
On CloudMan's Admin page (i.e., instance ip/cloud/admin) you can add the
email address you registered with in Galaxy on your cloud instance in the
'add galaxy admin' box and click add. After Galaxy restarts, you will have
become an admin on that instance.
Best,
Enis
On Sep 29, 2013 10:04
Hi Deniz,
Resizing the data volume via the main CloudMan page is fixed now and will
work for any newly created cluster.
On Thu, Aug 29, 2013 at 8:40 AM, Enis Afgan afg...@gmail.com wrote:
Sorry to hear you're having trouble Deniz. I've just tried to replicate
the issues and wanted to check
Hi Anto,
This has now been fixed for any new cluster. Sorry for the trouble and let
us know if you have any more questions.
Cheers
On Aug 9, 2013 5:06 PM, Anto Praveen Rajkumar Rajamani a...@hum-gen.au.dk
wrote:
Hello,
I have started a new cloudman instance.
Now, I am trying to upload my
FTP issues are fixed now so things will be functional out of the box
without any of these workarounds.
On Tue, Jul 16, 2013 at 4:04 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch
to create your instance, it
Hi Moritz,
I'm forwarding your message to galaxy-user mailing list and Jennifer from
Galaxy. Between the two, you should be able to get some help because
unfortunately this is not my area of expertise so I'm afraid I won't be of
much help.
Good luck,
Enis
-- Forwarded message --
H Jim,
The components for the cloud version are built in an automated fashion
using CloudBioLinux scripts (https://github.com/chapmanb/cloudbiolinux) so
maybe using those can get you closer to what you're after?
Cheers,
Enis
On Wed, Mar 6, 2013 at 5:17 AM, James Vincent j...@uvm.edu wrote:
Hi Zeeshan,
In order to gain from the scalability of the cloud, SGE does need to run.
However, CloudMan sets all that up and manages it going forward.
Enis
On Fri, Feb 8, 2013 at 8:59 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote:
Hi,
It seems that cloud man need SGE for scaling . Does SGE
Hi Nuphar,
I believe yu should be using a tool that is color-space aware and not
converting the data - Galaxy Main has 'Bowtie for SOLID' available, which
should understand your data as is.
BTW, for these types of questions, you should send the email to galaxy-user
mailing list
*We just released an update to CloudMan.* CloudMan offers an easy way to
get a personal and completely functional instance of Galaxy in the cloud in
just a few minutes, without any manual configuration.
*This update brings a large number of updates and new features, the most
prominent ones
With a certain version of Python there's been an issue stopping Galaxy
using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in
the background and then 'sh run.sh --stop-damemon' to stop it.
Hope this helps,
Enis
On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari
)) and the Galaxy set for
cluster(http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster).
We need Galaxy for large biological data quickly (faster than a stand
alone machine).
Maybe we do not understand something?
Best regards,
Anatoly
2012/10/3 Enis Afgan eaf...@emory.edu
Yes
Added: worker nodes are now submit hosts as well:
https://bitbucket.org/galaxy/cloudman/changeset/b4c66783b42fb559b35b689363b34826d00ced34
This will be generally available with the next release of CloudMan is made
(however, there is no immediate plans for doing so as quite a bit of other
details
Hi Lilach,
It seems you ran into a bug that was introduced in the most recent CloudMan
update. It's been fixed now.
If you still have your instance up, the way to get around the issue is to
simply strip off '/cloud' part of the URL and you'll get to Galaxy. Any new
instances will work fine.
*We just released an update to CloudMan.* CloudMan offers an easy way to
get a personal and completely functional instance of Galaxy in the cloud in
just a few minutes, without any manual configuration.
*This update brings a large number of updates and new features, the most
prominent ones
Hi Zeeshan,
The file system error message you saw when you first start a new cluster
is, oddly enough, the expected behavior. And, like you noticed, after the
cluster has been initialized for the first time, subsequent startups do not
show the error.
Enis
On Thu, May 10, 2012 at 4:11 AM, Zeeshan
Also Greg
Starting a new cloudman instance with a different cluster name than
previously used will always give you a clean environment and setup so you
can continue to always use the us-east region.
Cheers,
Enis
On 10/03/2012 2:08 PM, Ross ross.laza...@gmail.com wrote:
Since Dannon is likely
Hi John,
Theoretically, this is a straightforward task but in reality CloudMan
gets in the way of making it stick. Namely, if you are to manually
remove the master instance from being an execution host, CloudMan will
add it back in the next time a node is added or removed from the
cluster, thus
Hi Arthur,
Any tools run on main.g2.bx... are only stored on that server and not on
your local machine. By clicking on the Save icon (floppy disk) in your
history item, you are able to transfer the data from the remote server to
your local machine.
As far as your local installation goes - the
Hi Dave,
Sorry to hear you're having trouble and no, the behavior you describe is
not the expected behavior.
From the description, unfortunately it does not sound like adding more
nodes will help the case.
Could you take a look at the log files for Galaxy and see if anything there
is indicating
Hi again Greg,
On Tue, Jan 24, 2012 at 2:51 PM, mailing list margeem...@gmail.com wrote:
Hi guys,
So I'm trying to take a bioinformatics pipeline we currently run on
our own SGE cluster (which seems to have a lot of customizations ! I'm
finding out) and I want to run it on Amazon using
.
Would it be possible for the user to enter their zone on the form? Or
could CloudMan detect a problem, shutdown and try a different zone?
(probably infeasible).
Thanks again,
Greg
On Tue, Jan 24, 2012 at 9:08 AM, Enis Afgan afg...@gmail.com wrote:
Hi Greg,
This sounds like the availability
Hi Greg,
This sounds like the availability zone issue. I am assuming you are
restarting the same cluster (i.e., using the same name) and the instance
that gets created may be created in a zone different from the one that the
volume from the previous instantiation of the cluster was in.
Hi Greg,
Galaxy makes the tools more accessible by allowing web access to those
tools, it automatically handles job submission and management, as well as
allows simpler integration with other tools to form complex analyses.
Enis
On Thu, Jan 12, 2012 at 8:59 PM, mailing list margeem...@gmail.com
Hi Greg,
Please see below.
Two follow up questions:
1. Can I terminate my main instance, then start a new Cloudman
instance later and enter this share string to get back to where I was?
That would save some money vs stopping my main instance.
You should always terminate a cluster. Stopping
Hi Greg,
The color legend for the node status has been removed from the distribution
and replaced with the autoscaling option because it was too static to take
up that much screen space.
The icons should be easy to interpret standalone:
- blue: pending instance from AWS
- yellow: instance setup
group.
It probably makes sense to consolidate in one place so I'm continuing
the updates over there:
http://biostar.stackexchange.com/questions/15554/galaxy-cloudman-cant-get-an-instance-started-the-connection-has-timed-out
-Greg
On Sat, Dec 17, 2011 at 3:36 AM, Enis Afgan eaf
Hi Greg,
Sorry to hear you're having trouble.
Can you please confirm that you followed the step for creating a security
group on the wiki and opened all the specified ports?
Enis
On Fri, Dec 16, 2011 at 7:58 PM, mailing list margeem...@gmail.com wrote:
Hi Everyone,
I'm trying to set up Cloud
A new version of CloudMan for running Galaxy on Amazon cloud has been
released today. Any new cluster will automatically use this version.
Existing clusters will have a link displayed at the top of the CloudMan
console offering to perform an automated update.
The new version brings the following
Hi Clare,
Jeremy (from the team) ran a similar workshop several months ago and used
some resource intensive tools (e.g., Tophat). We were concerned about the
same scalability issues so we just started 4 separate clusters and divided
the users across those. The approach worked well and it turned
Hi Clare,
Sorry about the trouble. I just disabled that if statement in the template
so the option should no longer be disabled for any new cluster. My goal was
to simplify usage but I'll obviously have to revisit the implementation...
Sorry for the trouble and good luck with the demo tomorrow.
Hi Lizex,
The AWS pricing page has the prices for consuming their cloud resources:
http://aws.amazon.com/ec2/#pricing
As the model suggests, the total price will depend on your usage - at the
minimum, you'll need 1 instance for the duration of your computation and an
EBS volume to hold your data.
Hello all,
A new version of CloudMan has just been released. The two most prominent
changes in this release include:
1. Support for automated persistance of modifications to the underlying file
systems
2. Support for CloudBioLinux clusters on Ubuntu 11.04
-
1. CloudMan has
Hi Luciano,
Did you first create the galaxyWeb security group? Instructions are
available on usegalaxy.org/cloud under Step 1.
Enis
On 7/18/11 2:37 PM, Luciano Cosme wrote:
Hi,
I am trying to run Galaxy in the cloud and I am following your
screencast. I am having a problem when I need
By default, on cluster termination and restart everything is reverted to the
state the cluster was initially in.
However, if you'd like to customize your instance by adding tools and such,
it is possible. The document describing the procedure is available here:
Hi Joe,
This is by design. In order to change the settings in universe_wsgi.ini, you
should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This
file get pulled in by Cloudman each time an instance starts.
As far as restarting Cloudman, there is a (new) Admin panel (link at top
--
*From:* Enis Afgan [eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 11:46 AM
*To:* Joseph Hargitai
*Cc:* galaxy-user@lists.bx.psu.edu
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
Hi Joe,
This is by design. In order to change the settings in universe_wsgi.ini
however the Cloudman Admin tab you are referring to. Is this a
version issue?
we use: galaxy-cloudman-2011-03-22 (ami-da58aab3)
I do have the Admin tab in galaxy itself, but I do not think that is what
you are referring to.
joe
--
*From:* Enis Afgan [eaf
-da58aab3)
I do have the Admin tab in galaxy itself, but I do not think that is what
you are referring to.
joe
From: Enis Afgan [eaf...@emory.edu]
Sent: Tuesday, June 28, 2011 3:30 PM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] cloud instance
On Tue, Jun 28, 2011 at 6:38 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu wrote:
throws this:
{updated: false}
--
*From:* Enis Afgan [eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:02 PM
*To:* Oliver Hofmann; Joseph Hargitai
*Cc:* galaxy-user
Hi Joe,
We have not tried aspera (if I recall correctly, they're not open source?).
At the University of Chicago, though, there has been some work on enabling
Galaxy on the cloud to work with GridFTP and GlobusOnline, which is somewhat
related. There is a talk and PPT about that available at
Hi Thomas,
It turns out you discovered a bug in the cloud setup. We're missing a 2bit
file and a respective reference to the file for the extract genomic DNA
tool. We'll update the deployment but in the mean time you can configure the
instance yourself with just a few commands:
# connect to the
...@yahoo.com wrote:
Hello again,
So I am able to see all of the .dat files in /mnt/galaxyData. What
commands can I use to download a file to my HD? Also, what program should I
use to open the .dat file?
Thanks again,
Mike
--- On *Wed, 4/13/11, Enis Afgan eaf...@emory.edu* wrote:
From: Enis
step closer.
Thanks again,
Mike
--- On *Fri, 4/15/11, Enis Afgan eaf...@emory.edu* wrote:
From: Enis Afgan eaf...@emory.edu
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: Mike Dufault dufau...@yahoo.com
Cc: galaxy-u...@bx.psu.edu
Date: Friday, April 15, 2011, 8:21 AM
Yes it is - where you access the cloud console or Galaxy from has no affect
on running of the jobs.
Enis
On Thu, Apr 14, 2011 at 12:01 PM, Mike Dufault dufau...@yahoo.com wrote:
Hi,
I have an instance of Galaxy running on AWS. I would like to view it's
progress throughout the day, but I am
Hi Mike,
Try accessing your Galaxy instance now. It should be ok.
The link in your email contained the IP for your instance so I took the
liberty of restarting Galaxy and that brought it back up. There seems to
have been an issue with Galaxy accessing its database and that resulted in
Galaxy
if the analysis would be compromised.
Thanks again to you and the whole Galaxy team.
Best,
Mike
--- On *Tue, 4/12/11, Enis Afgan eaf...@emory.edu* wrote:
From: Enis Afgan eaf...@emory.edu
Subject: Re: [galaxy-user] Help!! with Galaxy Cloud!
To: Mike Dufault dufau...@yahoo.com
Cc
Hi Karl,
Hmm, not having Galaxy accessible is definitely not a step in the right
direction.
Being signed into command line is not an issue; something else must have
gone wrong. To start, please take a look at the (bottom of) galaxy log file
(and email the relevant part if you don't see how to fix
You're almost there, the command should be executed from your local machine
(home directory is fine) and it should look as follows:
scp -i path to keyfile
ubuntu@publicDNS:/mnt/galaxyData/files/000/dataset_11.dat
.
(note the 'ubuntu@' before the public DNS and a trailing dot (.) - the dot
means
, 2011, at 2:27 PM, Enis Afgan wrote:
Hi Luqman,
Take a look a my comments below.
On Fri, Mar 25, 2011 at 5:06 PM, Luqman Hodgkinson luq...@berkeley.eduwrote:
Hi Enis,
Thank you for your detailed reply. After playing with Galaxy, there are
some questions I have.
1. All my Java
. That should give you a good
indication of whether available functionality can be applied in your
scenario as well.
Enis
Sincerely, with best wishes,
Luqman
On Mar 25, 2011, at 10:21 AM, Enis Afgan wrote:
Hi Luqman,
Were you planning on using Galaxy CloudMan (usegalaxy.org/cloud
Thanks Dan. The revision of Galaxy is the problem - the instance of Galaxy
on the cloud is a month old now; it is at revision 5064 so.
I'll release an update in the coming days along with an updated CloudMan.
Enis
On Mon, Mar 14, 2011 at 11:24 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi
Hi Karl,
As a quick check, are the permissions for the S3 file set so anyone can read
the file? That's required before Galaxy's upload tool will be able to access
the file.
Alternatively, if you don't want to set such loose permissions, you should
be able to get a a signed URL for the given file
We'd like to announce an update to Galaxy CloudMan - a completely standalone
version Galaxy on Amazon's cloud.
The new version has been released that brings a number of improvements to
the core functionality of CloudMan and expands the number of tools available
within Galaxy CloudMan to match that
56 matches
Mail list logo
